Purpose – Smallholder farmers often deal with lack of information and knowledge, weak financial capacity and limited collaboration and network orientation. This is hampering their ability to adopt or co-develop innovation, and to participate in value chain exchanges. This calls for using intermediary organizations. The purpose of this paper is to understand how innovation intermediaries engage with smallholder farmers and provoke value chain reconfigurations. Design/methodology/approach – The authors systematically review literature to draw cases on intermediaries operating in the agri-food sector in several geographical and socio-economic contexts. The authors then adopt a theory building from cases approach to identify relationships between smallholder farmers and innovation intermediaries, and their effects in the reconfiguration of value chains. Findings – Consultants, knowledge transfer organizations (KTOs) and broker organizations (BOs) are the three typologies of intermediaries identified. While consultants facilitate change by modifying the way smallholders engage in transactions with their buyers and input providers, KTOs focus on farmers engagement in the value chain by stimulating the formation of knowledge platform or partnership. BOs operate in a similar way as compared to KTOs but mainly by forming and facilitating access to informal networks. Practical implications – The authors build a framework in which relationships between typologies of intermediary organizations and types of innovation processes are connected with changes at value chain level. Originality/value – The authors highlight how diverse forms of intermediations may stimulate not only smallholder farmers’ participation in innovation networks but also value chain reconfigurations.